I think megathreads are useful for things like an album release or a weekly episode release. It gives a place for conversation to occur without flooding the community with duplicate posts. I think the megathreads you're referring to though are the ones where it's like "New DIY-ers, ask questions here!" I agree that those should stay gone. No one reads them and they aren't helpful.
Coming from a moderation side, they were a consequence of users never bothering to search for answers to their problems and the fact that reddit search is fucking awful. If you just allowed every little question to get posted, the sub would suck and that's all users would see The only real solution was megathreads.